Keywords
Antiviral peptides, COVID-19, SARS-CoV-2, nCoV-19, peptide design, ACE2, Spike protein
This article is included in the Emerging Diseases and Outbreaks gateway.
This article is included in the Coronavirus (COVID-19) collection.
Antiviral peptides, COVID-19, SARS-CoV-2, nCoV-19, peptide design, ACE2, Spike protein
The world is currently experiencing the severe coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 or novel corona virus (nCoV) that originated from the Wuhan city, China1,2, and spread across the world. So far, two million people have been infected and more than 120,000 deaths are recorded across the globe. The death rate is 3–20% depending on the countries and the most affected countries are the USA, Italy, Spain, the UK and France, which have each recorded more than 10,000 deaths within a couple of weeks (WHO COVID-2019 situation reports). SARS-CoV-2 is highly contagious in humans and so far no medicine or vaccine has been developed to tackle the virus, making it impossible to control its spread across the globe3. Although drugs like hydroxychloroquine, remdesivir, and lopinavir4 are currently being suggested to treat COVID-19 infection, there is no clinical study so far to prove their efficacy in treating these patients. Therefore, currently there is a global search for appropriate drug and vaccine candidates against SARS-CoV-2.
SARS-CoV-2 has shown 80% genome identity with SARS-CoV, which is the causal agent of severe acute respiratory syndrome (SARS) seen in 2002–20035. SARS-CoV binds to the human angiotensin-converting enzyme 2 (hACE2) receptor through its Spike protein (S) to enter into the host cell6, and it is now reported that SARS-CoV-2 also binds to ACE2 to transmit its genetic material to human cells7–9. Therefore, blocking the Spike protein of SARS-CoV-2 could be an attractive and effective way to prevent the SARS-CoV-2 infection.
The crystal structure of the hACE2 receptor and the receptor binding domain (RBD) of the SARS-CoV-2 Spike protein (nCoV-RBD) (PDB: 6M17>) showed that a total of eight residues, namely, Gln24, Asp30, His34, Tyr41, Gln42 in α1 helix, Met82 in α2 helix, and Lys353 and Arg357 in the β3 and β4 linkers, are important for the binding9. The important interactions between the nCoV-RBD with ACE2 are Lys417 (Spike) --Asp30 (hACE2), Tyr453 (Spike) --His34 (hACE2), Gln474 (Spike) --Gln24 (hACE2), Phe486 (Spike) --Met82 (hACE2), Gln498 (Spike) --Tyr41 (hACE2), Thr500 (Spike) --Gln42 (hACE2), and Asn501 (Spike) --Lys3539.
Peptide-based drugs are a better choice than conventional drugs due to their higher efficiency, lesser molecular weight, and lower toxicity and side effects10. In this regard, antiviral peptides (AVPs), and a subset of antimicrobial peptides (AMPs), are of specific interest due to their higher efficacy in inhibiting viral infection by targeting various stages of the viral life cycle. AVPs can directly invoke innate immune response11 and inhibit viral entry by targeting viral attachment and entry to host cell, and replication, transcription, translation, multiplication, and release inside the host cell12,13. Previously, several AVPs have been reported to inhibit the SARS-CoV Spike protein or viral entry14–16.
In this report, using bioinformatics strategies, we attempted to design anti-Spike peptides for SARS-CoV-2 towards motivating potential therapeutics against the SARS-CoV-2 infection.
We adopted three strategies to predict potential AVPs against the SARS-CoV-2 Spike protein.
In the first strategy, we re-analysed the SARS-CoV-2 Spike RBD with hACE2 to identify the key interacting residues in both the proteins. A recent report suggests that the B chain of SARS-CoV-2 Spike protein interacts with the B or D homodomain of hACE29. Therefore, in this analysis, we used the individual B chain of SARS-CoV-2 Spike RBD (PDB: 6LZG) and the B chain of hACE2 (PDB: 6M18) to dock with each other using the HADDOCK 2.2 server17, providing active residues of both the proteins as described by Yan et al., (2020)9 and using default parameters. Based on the binding interactions and based on previous reports9, we identified the key interacting residues. In the next step, we designed a number of AVPs based on the interacting hACE2 residues to the RBD of the Spike protein. To design the AVPs, we used simple permutation and combination approach of amino acids, keeping the key interacting amino acids and their positions fixed in the peptide. Binding to SARS-CoV-2 Spike RBD with the designed AVPs was determined by the HPEPDOCK protein-peptide docking server18. For the HPEPDOCK analysis, we used the SARS-CoV-2 Spike RBD (PDB: 6LZG) B chain and the sequence of the peptides in FASTA format, specifying eight binding sites (Lys417, Tyr453, Gln474, Phe486, Gln493, Gln498, Thr500, and Asn501) of Spike-RBD9 and 100 peptide binding mode. The final peptides were selected based on their HPEPDOCK docking energy score, number of binding sites, number and position of selected target residue binding, physiochemical properties, and AVPpred prediction13. More negative binding energy and the number and position of residue binding sites were given more importance in selecting the final peptides (described in Results).
In the second strategy, we screened the available anti-microbial peptides (AMPs) against the SARS-CoV-2 Spike RBD. We used the database of antiviral peptides (AVPdb)19, database of HIV inhibitory peptides (HIPdb)12, Antimicrobial Peptide Database (APD3)20, database of anti-microbial peptides (dbAMP)21, and database of FDA-approved peptide and protein therapeutics (THPdb)22 and screened the peptides against the SARS-CoV-2 Spike RBD. In this process, we collected all the AMP sequences from these databases and then each peptide was docked against the Spike-RBD using the HPEPDOCK protein-peptide docking server18. The process and the parameters of HPEPDOCK docking and selection of peptides were the same as used in first strategy.
In the third strategy, we adopted a chimeric peptide design approach where the two fragments of two different peptides selected in our previous two approaches are composed in such a way that the resultant peptide can bind to our given target residues in the SARS-CoV-2 Spike RBD. In this approach, we first selected the peptides that bind to any of the three key residues (Phe486, Gln493, and Asn501) of the Spike RBD. Next, we took various lengths of fragments of these peptides (4–15) that interact with the key residues of Spike RBD. Next, we joined these peptides keeping the key residue position fixed to make chimeric peptides of 20–25 amino acids in length. In these peptides, various permutations and combinations of amino acids were made, keeping the key interacting amino acids and their positions fixed. A total of 500 such chimeric peptides were designed and docked with Spike RBD target residues (Lys417, Tyr453, Gln474, Phe486, Gln493, Gln498, Thr500, and Asn501) using the HPEPDOCK server18 as described in the first strategy . The final peptides were selected based on similar criteria as adopted in the first and second strategy.
Antiviral properties of the peptides were predicted using AVPpred13 using its default parameters. The molecular formula, molecular weight, net charge, grand average hydropathy, total hydrophobic ratio, hydrophobicity, and protein-binding potential (Boman index) were calculated using the APD3 antimicrobial peptide calculator and predictor20. The IC50 of the peptides was predicted using the AVP-IC50Pred server, selecting the RSV/INFV/HSV prediction model23 and other default parameters. Hemolytic potency of peptides was determined using the HemoPI server24 with default parameters, where the values tending towards “0” are unlikely to be hemolytic. ToxinPred25, with default parameters, was used to predict the toxicity (toxic or non-toxic) of the peptides. The final peptides were selected based on their: HPEPDOCK docking energy score (cut-off -120 or less), number of H bonds (>2), number of selected target residue bonds (2-10), number of key target residue bonds (>2), physiochemical properties (parameters acceptable for AMPs, see Extended data26), and AVPpred prediction (Yes)13.
In SARS-CoV-2 Spike RBD - hACE2 interaction analysis, similar to Yan et al. (2020)9, we found that three stretches of peptides that harbour the active residues of hACE2 interact with Spike RBD. These stretches have amino acid positions: 21-43 (five sites), 78-87 (one site), and 348-361 (two sites). In the Spike RBD, the key interacting amino acid stretches are 480-489 and 490-505. A previous report suggests that among the Spike residues, the most important residues interacting with hACE2 are Phe486, Gln493, and Asn50127. An in-depth analysis revealed that any peptide that potentially blocks the Spike RBD should bind at least three critical positions of the RBD: (i) Gly485 or Phe486 or Asn487, (ii) Gln493, and (iii) Gln498 or Thr500 or Asn501 among which the Phe486, Gln493, and Asn501 are essential.
We designed three peptides from the first stretch of the hACE2 that shows maximum active binding residues with the Spike RBD. A 26 amino acid peptide (AC26) binds to Thr500 and Asn501 of the Spike RBD (Figure 1A), a 23 amino acid peptide (AC23) binds to Tyr489 and Thr500 of the Spike RBD (Figure 1B), and a third 20 amino acid peptide (AC20) binds to Gln493 and Asn501 of the Spike RBD (Figure 1C). All these peptides show acceptable physiochemical properties to be used as therapeutic peptides (see Extended data26). However, none of these three peptides are able to block all the key three positions of the Spike RBD. Therefore, these peptides may not be suitable for developing very effective anti-SARS-CoV-2 therapeutics targeting its Spike RBD. However, AC20 and AC23 can be further tested.
We identified seven peptides by screening the five different AMP databases. It is known that SARS-CoV directly interacts with hACE2 through their RBD located in the B chain of the Spike protein28,29 and the Spike protein sequence of SARS-CoV-2 is highly similar to SARS-CoV8 and SARS-related coronaviruses. In our peptide database analysis, we also observed that the peptides that have been experimentally proven to be effective against SARS-CoV have the potential of being used against the SARS-CoV-2 Spike protein. All of the seven identified peptides (see Extended data26) are of 20 amino acids in length and are reported to target the Spike protein of SARS-CoV to exhibit their anti-SARS virus activities19. Although the peptides show four to 11 “H” bonds and form between two to four bonds with our eight given target residues, most of these peptides do not bind to all the three positions ((i) Gly485 or Phe486 or Asn487, (ii) Gln493, and (iii) Gln498 or Thr500 or Asn501) to effectively block the Spike RBD.
The DBP1, DBP2, and DBP3 peptides bind to only the third position (Gln498 and Asn501) of the Spike RBD without binding to the other two sites (Figure 2A–C; Extended data26). DBP4, DBP5, and DBP7 interact with the first (Gly485 or Phe486 or Asn487) and third (Gln498 and Asn501) sites of the Spike RBD without binding to the middle or the second site (Gln493) (Figure 2D, E, G; Extended data26). DBP6 binds to all the three sites within the range of the target residues but does not interact with the key residues of the first and third sites (Figure 2F; Extended data26). DBP6 is also predicted to be an antiviral peptide by AVPpred13. Therefore, DBP6 could be a potential peptide to be tested for SARS-CoV-2 Spike protein-based drug development.
Out of 500 chimeric peptides generated, only seven were selected for final analysis. All these peptides are non-hemolytic, non-toxic, and meet all the criteria of a therapeutic peptide (see Extended data26). Among these seven peptides, cnCoVP-3, cnCoVP-4, and cnCoVP-7 interact with all the three sites and two key residues of the second (Gln493) and third (Asn501) sites. However, these peptides bind one amino acid apart from the key residue (Phe486) in the first site and potentially block the access of SARS-CoV-2 Spike Phe486 to the hACE2 (Figure 3C, D, G; Extended data26). AVPpred13 also predicted cnCoVP-4 to be an antiviral peptide. Therefore, these three peptides could be selected for further in vitro and in vivo testing.
Although the chimeric peptides cnCoVP-2, cnCoVP-5, and cnCoVP-6 interact with all the three sites, they do not interact with the key residue (Phe486) or the immediate to key residue of the first site. Instead they bind a residue that is two to three amino acids apart from the key residue (Phe486) (Figure 3B, E, F; Extended data26). Therefore, these three peptides may not block the first site of the Spike RBD in interacting with hACE2. However, they should also be synthesized and tested for their in vitro effects. The last peptide, cnCoVP-1, was found to interact with all the three sites; however, it only interacts with the key residue (Gln493) of the second site. In the other two sites, it interacts at position (Tyr489) of the first site and (Gln498) of the third site (Figure 3A; Extended data26). Although Gln498 is a key residue of the third site Tyr489, it is not an interacting residue in the original interaction between SARS-CoV-2 Spike RBD and hACE2. Thus, this peptide may partially block the access of SARS-CoV-2 Spike RBD to hACE2 and needs further in vitro and in vivo testing and validation.
In this article, we screened and designed several peptides that may potentially block the interaction between SARS-CoV-2 Spike RBD and hACE2. Ten peptides (AC20, AC23, DBP6, and cnCoVP-1- cnCoVP-7) have very high potential to achieve this interaction, indicating that these peptides could be attractive therapeutics against SARS-CoV-2. However, peptide synthesis, in vitro, and in vivo experiments are required to evaluate and ensure their potential therapeutic efficacy.
B chain of SARS-CoV-2 Spike RBD from PDB, Accession number 6LZG: https://identifiers.org/rcsb/pdb:6LZG
B chain of hACE2 from PDB, Accession number 6M18: https://identifiers.org/rcsb/pdb:6M18
Harvard Dataverse: Potential chimeric peptides to block the SARS-CoV-2 Spike RBD. https://doi.org/10.7910/DVN/WSDRTU26
This project contains the following extended data:
- MS_cnCoVP_Supplementary_Table-S1_F1000.xlsx (detailed physiochemical and docking properties and AVPpred prediction of each peptide)
Data are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
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Is the work clearly and accurately presented and does it cite the current literature?
Yes
Is the study design appropriate and is the work technically sound?
Yes
Are sufficient details of methods and analysis provided to allow replication by others?
Partly
If applicable, is the statistical analysis and its interpretation appropriate?
Not applicable
Are all the source data underlying the results available to ensure full reproducibility?
Partly
Are the conclusions drawn adequately supported by the results?
Yes
References
1. Ibrahim IM, Abdelmalek DH, Elshahat ME, Elfiky AA: COVID-19 spike-host cell receptor GRP78 binding site prediction.J Infect. 80 (5): 554-562 PubMed Abstract | Publisher Full TextCompeting Interests: No competing interests were disclosed.
Is the work clearly and accurately presented and does it cite the current literature?
Yes
Is the study design appropriate and is the work technically sound?
Yes
Are sufficient details of methods and analysis provided to allow replication by others?
Yes
If applicable, is the statistical analysis and its interpretation appropriate?
Yes
Are all the source data underlying the results available to ensure full reproducibility?
Yes
Are the conclusions drawn adequately supported by the results?
Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Molecular Biology, Cancer Stem Cell, Epigenetics, Nutrigenomics, Cancer Biology
Is the work clearly and accurately presented and does it cite the current literature?
Yes
Is the study design appropriate and is the work technically sound?
Yes
Are sufficient details of methods and analysis provided to allow replication by others?
Yes
If applicable, is the statistical analysis and its interpretation appropriate?
Yes
Are all the source data underlying the results available to ensure full reproducibility?
Yes
Are the conclusions drawn adequately supported by the results?
Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Pharmacogenomics
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